Biology subjects

Kurihara, K.

Publications and source records attributed to Kurihara, K..

8 recordsLinked to original sources

bioRxiv2026

SPATNIC enables H&E-grounded cancer-cell identification across spatial and single-cell transcriptomic modalities in colorectal cancer

Tumors contain diverse non-cancer cells that constitute the tumor microenvironment; thus, identifying which cells are cancerous is a foundational and critical first step in cancer research. However, to our knowledge, no transcriptome-based classifier has been trained using pathologist-defined annotations from matched H&E images at single-cell resolution. Moreover, few tools can be shared across diverse platforms. Here, we present SPATNIC, a variational autoencoder that classifies individual cells as cancer or normal, trained on Xenium cells labeled by a pathologist review of matched H&E images. It matches or exceeds the performance of existing tools in primary colorectal tumors and liver and lung metastases. SPATNIC generalizes zero-shot across Visium, Visium HD, CosMx, Xenium, MERSCOPE, and single-cell RNA sequencing. In public single-cell atlases, it identified a rare POU2F3 tuft-like cancer stem cell population missed by existing annotations and associated with worse survival. In rectal cancer profiled before and after chemoradiotherapy, it separated cancer from normal epithelium in tissue, thus enabling per-patient screening of antibody-drug conjugate (ADC) targets.

cancer biology↗

bioRxiv2026

Catalog of gut microbiota alterations associated with anticancer therapies across multiple cancer types

BackgroundAnticancer therapies can alter the gut microbiota and may affect gut bacteria associated with treatment response. However, most longitudinal studies have focused on specific cancer types or individual treatment regimens, and systematic analyses across diverse cancer therapies remain limited. We analyzed longitudinal fecal microbiota profiles using 16S ribosomal RNA gene amplicon sequencing in the pan-cancer SCRUM-Japan MONSTAR-SCREEN cohort. We included 528 paired pre- and post-treatment fecal samples from 264 patients with advanced solid tumors across 18 cancer types and characterized the gut microbiota alterations associated with 22 anticancer drugs and related clinical factors. ResultsAcross the cohort, Shannon diversity did not significantly change after treatment (mean, 3.81 vs. 3.78; P = 0.58), and pre- and post-treatment samples exhibited no clear separation in ordination space. However, within-patient analysis detected a subtle but significant longitudinal microbiota shift (paired PERMANOVA, P = 0.0001), highlighting the importance of accounting for paired sampling. Clustering of genus-level compositional alterations revealed patient groups with distinct degrees of microbiota alteration, with the largest shifts associated with antibiotic exposure, transition from normal stool to diarrhea, and specific treatment regimens. Multivariable regression analysis of 22 anticancer drugs identified drug-bacteria associations and demonstrated that drugs with similar mechanisms of action, including epidermal growth factor receptor (EGFR) inhibitors and immune checkpoint inhibitors, exhibited similar microbiota change profiles. Targeted analyses highlighted concordant reductions in the Christensenellaceae R-7 group among EGFR inhibitor-exposed patients and depletion of Faecalibacterium among immune checkpoint inhibitor-exposed patients. ConclusionsThis study provides a cross-cancer catalog of microbiota alterations associated with anticancer therapies and highlights therapy-related shifts in the gut ecosystem, including patterns shared by drugs with similar mechanisms of action.

microbiology↗

bioRxiv2026

Host innate immune response profiling reveals hidden viral infections across diverse animal species

Virus discovery using RNA-seq data from wildlife and livestock offers a powerful strategy for identifying unknown pathogens with pandemic potential. However, conventional approaches rely on homology-based searches that have limited sensitivity for highly divergent viruses, are computationally intensive at scale, and cannot distinguish true infections from contamination. Viral infection induces interferon-stimulated genes (ISGs), key components of the frontline antiviral defense, and their expression serves as a robust indicator of viral infection. Here, we developed a host-response-based virus discovery framework that rapidly quantifies ISG expression and predicts viral infection status. Applying this framework to [~]210,000 RNA-seq data sets from diverse mammalian and avian species, we identified hidden viral infections across diverse hosts, including those caused by highly divergent viruses missed by a conventional approach. Our framework complements existing virus discovery strategies by adding host innate immune response context and enabling computationally efficient prescreening for scalable viral surveillance. HighlightsO_LIHost response-based virus discovery in wildlife and livestock RNA-seq data C_LIO_LIQuantify interferon-stimulated gene (ISG) expression and predict viral infection C_LIO_LIAnalysis of [~]210,000 RNA-seq data sets reveals hidden viral infections C_LIO_LIDetects highly divergent viruses and scalable viral surveillance through rapid prescreening C_LI

microbiology↗

bioRxiv2025

Engineering a Covalent Linkage into a Dimeric De Novo Enzyme Reveals a Novel Life-Sustaining Mechanism

Designing novel proteins that share no homology with natural sequences, but which nonetheless provide life sustaining functions, is an important goal for synthetic biology. Towards this goal, we previously reported Syn-F4, the first de novo enzyme capable of catalyzing a life-sustaining reaction, both in vitro and in vivo. Syn-F4 catalyzes hydrolysis of the siderophore, ferric enterobactin, thereby releasing iron and enabling growth in iron-limited media of an otherwise inviable {Delta}fes strain of Escherichia coli. Although Syn-F4 provides a direct enzymatic replacement of the natural ferric enterobactin esterase encoded by Fes, it has a dramatically different structure and enzymatic mechanism than the natural Fes enzyme. The novel Syn-F4 enzyme forms a 4-helix bundle, comprising a homodimer of two -helical hairpins. Here we describe the engineering of a covalent peptide linkage into the homodimer to generate a single chain 4-helix bundle. As expected, the resulting linked protein (Syn-F4-Link) also rescued {Delta}fes cells in iron-limited media. Moreover, X-ray crystallography revealed a 3D structure similar to the parental homodimer. Surprisingly, however, the linked protein was not enzymatically active. Instead, Syn-F4-Link rescues {Delta}fes cells by upregulating biosynthesis of the enterobactin siderophore thereby enabling assimilation of sufficient iron to sustain cell growth. These findings demonstrate that two very similar de novo proteins can sustain cell growth using dramatically different biological mechanisms.

synthetic biology↗

bioRxiv2025

Epidermal Resident Memory T Cell Fitness Requires Antigen Encounter in the Skin

CD8+ tissue resident memory T cells (TRM) develop from effectors that seed peripheral tissues where they persist providing defense against subsequent challenges. TRM persistence requires autocrine TGF{beta} transactivated by integrins expressed on keratinocytes. TRM precursors that encounter antigen in the epidermis during development outcompete bystander TRM for TGF{beta} resulting in enhanced persistence. ScRNA-seq analysis of epidermal TRM revealed that local antigen experience in the skin resulted in an enhanced differentiation signature in comparison with bystanders. Upon recall, TRM displayed greater proliferation dictated by affinity of antigen experienced during epidermal development. Finally, local antigen experienced TRM differentially expressed TGF{beta}RIII, which increases avidity of the TGF{beta}RI/II receptor complex for TGF{beta}. Selective ablation of Tgfbr3 reduced local antigen experienced TRM capacity to persist, rendering them phenotypically like bystander TRM. Thus, antigen driven TCR signaling in the epidermis during TRM differentiation results in a lower TGF{beta} requirement for persistence and increased proliferative capacity that together enhance epidermal TRM fitness.

immunology↗

bioRxiv2023

Multi-pass, single-molecule nanopore reading of long protein strands with single-amino acid sensitivity

The ability to sequence single protein molecules in their native, full-length form would enable a more comprehensive understanding of proteomic diversity. Current technologies, however, are limited in achieving this goal. Here, we establish a method for long-range, single-molecule reading of intact protein strands on a commercial nanopore sensor array. By using the ClpX unfoldase to ratchet proteins through a CsgG nanopore, we achieve single-amino acid level sensitivity, enabling sequencing of combinations of amino acid substitutions across long protein strands. For greater sequencing accuracy, we demonstrate the ability to reread individual protein molecules, spanning hundreds of amino acids in length, multiple times, and explore the potential for high accuracy protein barcode sequencing. Further, we develop a biophysical model that can simulate raw nanopore signals a priori, based on amino acid volume and charge, enhancing the interpretation of raw signal data. Finally, we apply these methods to examine intact, folded protein domains for complete end-to-end analysis. These results provide proof-of-concept for a platform that has the potential to identify and characterize full-length proteoforms at single-molecule resolution.

biophysics↗

bioRxiv2023

Engineering a highly durable adeno-associated virus receptor for analytical applications

Adeno-associated virus (AAV) is a major viral vector used in gene therapy. There are multiple AAV serotypes, and many engineered AAV serotypes with modified capsids altering tissue tropism are enthusiastically being developed. The universal AAV receptor (AAVR) is an essential receptor for multiple AAV infections. Since most AAV serotypes used in gene therapy infect cells via interaction with AAVR, the quantification of the vector-binding ability of AAV to AAVR could be an important quality check for therapeutic AAV vectors. To enable a steady evaluation of the AAV-AAVR interaction, we created an engineered AAVR through mutagenesis. Engineered AAVR showed high durability against acid while retaining its AAV-binding activity and an affinity chromatography column with engineered AAVR was also developed. This column enabled repeated binding and acid dissociation measurements of AAVR with various AAV serotypes. Our data showed that the binding affinities of AAV to AAVR were diverse among serotypes, providing insight into the relationship with the infection efficiency of AAV vectors. Thus, this affinity column can be used in process development for quality checks, quantitating capsid titers, and affinity purification of AAV vectors. Furthermore, this column may work for a useful tool of novel AAV vector capsid engineering.

bioengineering↗

bioRxiv2022

Highly efficient protein expression of Plasmodium vivax surface antigen, Pvs25 by silkworm, Bombyx mori, and its biochemical analysis.

Plasmodium vivax ookinete surface protein, Pvs25 is a transmission-blocking vaccine (TBV) candidate for malaria. Pvs25 has four EGF-like domains containing 22 cysteine residues forming 11 intramolecular disulfide bonds and this structural feature makes recombinant expression of Pvs25 difficult. In this study, we report the high expression of recombinant Pvs25 as a soluble form in silkworm, Bombyx mori. The Pvs25 protein was purified from hemolymphs of larvae and pupae by affinity chromatography. In the Pvs25 expressed by silkworm, no isoform with inappropriate disulfide bonds was found, requiring no further purification step which is necessary in case of Pichia pastoris based expressions systems. The Pvs25 from silkworm were confirmed to be the molecularly uniform by sodium dodecyl sulfate gel electrophoresis analysis and size exclusion chromatography analysis. To examine the immunogenicity, the Pvs25 from B. mori, was administered to BALB/c mice by the subcutaneous (s.c.) route with the oil adjuvant. The Pvs25 produced by silkworm induced potent and robust immune response, and the induced antisera correctly recognized P. vivax ookinetes in vitro, demonstrating the potency of Pvs25 from silkworm as a TBV candidate for malaria. This is the first study that to construct a mass production system for malaria TBV antigens by the silkworm to the best of our knowledge.

biochemistry↗